Data file

We used the “CompRefBI_mzml_metricInfo_all_id.07272017.tsv” data file in this report. To see the data file in tsv format, please click

Here

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PDF file

To generate the PDF file of this report please run the following code in the R command line “rmarkdown::render(”./static_dv7_17.Rmd“, output_format=”pdf_document“)” To view the generated PDF file, please click

Here

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Number of MS2 spectra

Per sample, across fraction (boxplot) , without the same scale

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Per sample, across fraction (boxplot) , with the same scale

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Per sample, versus fraction (scatterplot), without the same scale

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Per sample, versus fraction (scatterplot), with the same scale

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Number of MS2 spectra versus fraction (boxplot), without the same scale

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Number of MS2 spectra versus fraction (boxplot), with the same scale

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Precursor intensity values

Range of Precursor intensity values For all spectra

This table shows the range of the precursor intensity for each percentile, as a summary and to see if there are any value of 0 that cannot be log-transformed

5th Perc 25th perc 50th perc 75th perc 95th perc
range 0, 0 13921.04, 2785124.75 50261.56, 8182241.5 140378.73, 20557060 1450821.96, 86219475.2
range of log10 transformed -Inf, -Inf 4.14, 6.44 4.7, 6.91 5.15, 7.31 6.16, 7.94

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Range of Precursor intensity values For identified spectra

This table shows the range of the precursor intensity for each percentile, as a summary and to see if there are any value of 0 that cannot be log-transformed
5th Perc 25th perc 50th perc 75th perc 95th perc
range 0, 105641.58 190316.07, 5425278 394277.41, 12651390 992609.34, 30232546 6000430.85, 131598537.6
range of log10 transformed -Inf, 5.02 5.28, 6.73 5.6, 7.1 6, 7.48 6.78, 8.12

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Per sample, versus fraction (scatterplot), with the same scale

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Percentage of 0 precursor intensities at different percentiles, For all spectra

In this table, each row represents a fraction and each column represents a percentile. Each value represents the percent of samples that have a precursor intensity of 0 at that fraction and that percentile.
5th Perc 25th Perc 50th Perc 75th Perc 95th Perc
fraction1 100 0 0 0 0
fraction2 100 0 0 0 0
fraction3 100 0 0 0 0
fraction4 100 0 0 0 0
fraction5 100 0 0 0 0
fraction6 100 0 0 0 0
fraction7 100 0 0 0 0
fraction8 100 0 0 0 0
fraction9 100 0 0 0 0
fraction10 100 0 0 0 0
fraction11 100 0 0 0 0
fraction12 100 0 0 0 0
fraction13 100 0 0 0 0
fraction14 100 0 0 0 0
fraction15 100 0 0 0 0
fraction16 100 0 0 0 0
fraction17 100 0 0 0 0
fraction18 100 0 0 0 0
fraction19 100 0 0 0 0
fraction20 100 0 0 0 0
fraction21 100 0 0 0 0
fraction22 100 0 0 0 0
fraction23 100 0 0 0 0
fraction24 100 0 0 0 0
fraction25 100 0 0 0 0

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Percentage of 0 precursor intensities at different percentiles, For identified spectra

In this table, each row represents a fraction and each column represents a percentile. Each value represents the percent of samples that have a precursor intensity of 0 at that fraction and that percentile.
5th Perc 25th Perc 50th Perc 75th Perc 95th Perc
fraction1 100.000 0 0 0 0
fraction2 100.000 0 0 0 0
fraction3 100.000 0 0 0 0
fraction4 100.000 0 0 0 0
fraction5 100.000 0 0 0 0
fraction6 100.000 0 0 0 0
fraction7 100.000 0 0 0 0
fraction8 100.000 0 0 0 0
fraction9 100.000 0 0 0 0
fraction10 100.000 0 0 0 0
fraction11 100.000 0 0 0 0
fraction12 100.000 0 0 0 0
fraction13 66.667 0 0 0 0
fraction14 100.000 0 0 0 0
fraction15 100.000 0 0 0 0
fraction16 100.000 0 0 0 0
fraction17 100.000 0 0 0 0
fraction18 100.000 0 0 0 0
fraction19 100.000 0 0 0 0
fraction20 100.000 0 0 0 0
fraction21 100.000 0 0 0 0
fraction22 100.000 0 0 0 0
fraction23 100.000 0 0 0 0
fraction24 100.000 0 0 0 0
fraction25 0.000 0 0 0 0

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Precursor m/z values

Per sample, versus fraction (scatterplot), without the same scale

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Per sample, versus fraction (scatterplot), with same scale

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Precursor Molecular weight (MW) values

Per sample, versus fraction (scatterplot), without the same scale

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Per sample, versus fraction (scatterplot), with the same scale

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Per sample, across fraction at 50 percentile (boxplot), without the same scale

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Per sample, across fraction at 50 percentile (boxplot), with the same scale

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Per sample, across fraction (boxplot), without the same scale

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Per sample, across fraction (boxplot), with the same scale

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MS2 per MS1 values

Per sample, versus fraction (scatterplot), without the same scale

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Per sample, versus fraction (scatterplot), with the same scale

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Median of MS2 per MS1 value for all spectra

In this table, the meidian MS2 per MS1 value is present, each column represent a different percentile.
The median of MS2 per MS1
5th Perc 25th Perc 50th Perc 75th Perc 95th Perc
00CPTAC_P5P6CompRef_W_BI_20160623_BL 0 0 2 6 14
01CPTAC_CompRef_W_BI_20160908_BL 0 0 2 8 15
02CPTAC_CompRef_W_BI_20161028_BL 0 0 2 7 15

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Median of MS2 per MS1 value for identified spectra

In this table, the meidian MS2 per MS1 value is present, each column represent a different percentile.
The median of MS2 per MS1
5th Perc 25th Perc 50th Perc 75th Perc 95th Perc
00CPTAC_P5P6CompRef_W_BI_20160623_BL 0 0 1 3 6
01CPTAC_CompRef_W_BI_20160908_BL 0 0 1 3 6
02CPTAC_CompRef_W_BI_20161028_BL 0 0 1 3 6

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Table of values less than 20 for all spectra

In this table the percent for the values less than 20 are present, each column is a different percentile
Percent of samples’ value less than 20
5th Perc 25th Perc 50th Perc 75th Perc 95th Perc
00CPTAC_P5P6CompRef_W_BI_20160623_BL 100 100 100 100 100
01CPTAC_CompRef_W_BI_20160908_BL 100 100 100 100 100
02CPTAC_CompRef_W_BI_20161028_BL 100 100 100 100 100

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Table of values less than 20 for identified spectra

In this table the percent for the values less than 20 are present, each column is a different percentile
Percent of samples’ value less than 20
5th Perc 25th Perc 50th Perc 75th Perc 95th Perc
00CPTAC_P5P6CompRef_W_BI_20160623_BL 100 100 100 100 100
01CPTAC_CompRef_W_BI_20160908_BL 100 100 100 100 100
02CPTAC_CompRef_W_BI_20161028_BL 100 100 100 100 100

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Different MS2 charge state to MS2 charge 2 ratio

Per sample, versus fraction (scatterplot), without the same scale

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Per sample, versus fraction (scatterplot), with the same scale

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